diff variant_effect_predictor/Bio/DB/Flat/BDB/fasta.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/DB/Flat/BDB/fasta.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,86 @@
+#
+# $Id: fasta.pm,v 1.3 2002/10/22 07:38:31 lapp Exp $
+#
+# BioPerl module for Bio::DB::Flat::BDB
+#
+# Cared for by Lincoln Stein <[e-mail]>
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::DB::Flat::BDB::fasta - fasta adaptor for Open-bio standard BDB-indexed flat file
+
+=head1 SYNOPSIS
+
+See Bio::DB::Flat.
+
+=head1 DESCRIPTION
+
+This module allows fasta files to be stored in Berkeley DB flat files
+using the Open-Bio standard BDB-indexed flat file scheme.  You should
+not be using this directly, but instead use it via Bio::DB::Flat.
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to one
+of the Bioperl mailing lists.  Your participation is much appreciated.
+
+  [e-mail]             - General discussion
+  http://bioperl.org/MailList.shtml - About the mailing lists
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+the bugs and their resolution.  Bug reports can be submitted via
+email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 SEE ALSO
+
+L<Bio::DB::Flat>,
+
+=head1 AUTHOR - Lincoln Stein
+
+Email - [e-mail]
+
+=cut
+
+package Bio::DB::Flat::BDB::fasta;
+
+use strict;
+use Bio::DB::Flat::BDB;
+use vars '@ISA';
+
+@ISA = qw(Bio::DB::Flat::BDB);
+
+sub parse_one_record {
+  my $self  = shift;
+  my $fh    = shift;
+
+  undef $self->{fasta_stored_id} if exists $self->{fasta_stored_fh}
+    && $fh ne $self->{fasta_stored_fh} ;
+  $self->{fasta_stored_fh} = $fh;
+
+  while (<$fh>) {		# don't try this at home
+    if (/^>(\S+)/) {
+      my $id = $self->{fasta_stored_id};
+      $self->{fasta_stored_id} = $1;
+      next unless defined $id;
+      return ($id,-length($_));
+    }
+  }
+  # we get here at the end of the file
+  return $self->{fasta_stored_id};
+}
+
+sub default_file_format { "fasta" }
+
+1;